Re: [HCP-Users] Converting legacy data to CIFTI format

[Glasser, Matthew]

That doesn’t sound like you solved the alignment problem (it will still be 
misaligned in the volume) and I wouldn’t expect specifying the T2w as the T1w 
will work without some pipeline modifications.

Matt.

From: Kelli Cannon >
Date: Thursday, October 6, 2016 at 1:17 PM
To: Matt Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: Converting legacy data to CIFTI format

Hi Matt,

Thanks for the information! I was able to successfully run the PreFreeSurfer 
pipeline by specifying the T1w image as the T2w image. The FreeSurfer pipeline 
is running now, and I expect to be able to run the PostFreeSurfer pipeline 
next, since I have the output files from the PreFreeSurfer pipeline to use as 
inputs into the PostFreeSurfer pipeline.

The main reason that I am wanting to convert my legacy data into CIFTI space is 
to map the Glasser et al., 2016 MMP average parcellation scheme to my data. 
Since the lack of field maps makes accurately registering the BOLD scan to the 
T1w image problematic, I will apply the subject-specific NIFTI/CIFTI 
transformation matrix to the parcellated CIFTI file in order to map the parcels 
onto the subject’s volume space and then do my analysis of the BOLD data in 
volume space.

Thanks again for the help!

Best,
Kelli


On Oct 4, 2016, at 5:35 AM, Glasser, Matthew 
> wrote:

The lack of a field map is the larger issue, as it makes accurately registering 
the EPI to the T1w image problematic.  Some folks have made use of an “average 
field map” to attempt to improve upon this situation, but I don’t have this 
code or personal experience with this.

Lacking the T2w image need not necessarily prevent mapping fMRI data to CIFTI 
as one can take the non T2w parts of PreFreeSurfer (basically everything except 
the T2w to T1w registration and the bias correction), do things like specifying 
the T1w image as the T2w image (e.g. for the MNI registration), run FreeSurfer 
on its own, and then specify the T1w image as the T2w image for PostFreeSurfer. 
 A script that does all of this exists, but is not an “official pipeline.”

Peace,

Matt.

From: Kelli Cannon >
Date: Monday, October 3, 2016 at 5:32 PM
To: "hcp-users@humanconnectome.org" 
>
Cc: Matt Glasser >
Subject: Converting legacy data to CIFTI format

Hello,

I would like to convert a legacy dataset into CIFTI format. The legacy dataset 
lacks T2-weighted images or field maps. How does the HCP advise that 
investigators go about converting legacy data into CIFTI format? I assume this 
must be possible, as we can use FreeSurfer to convert to flat maps with such 
data...

For the structural data, the PreFreeSurfer pipeline requires both a T1w and a 
T2w image, so it can not be used on the legacy dataset. One can run the T1w 
images through FreeSurfer’s recon-all to approximate the HCP FreeSurfer 
pipeline for lower-resolution data. However, the PostFreeSurfer pipeline 
requires additional input files (e.g., T1w_acpc_dc_restore.nii.gz) that are not 
included in the FreeSurfer output.

Is there a reasonably straightforward way of converting legacy data without T2w 
images into CIFTI format? If not, does HCP plan to create a pipeline for 
preprocessing legacy data?


Best regards,

Kelli Cannon
Graduate Student
UAB Department of Vision Science
kecan...@uab.edu




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Re: [HCP-Users] Converting legacy data to CIFTI format

[Glasser, Matthew]

The lack of a field map is the larger issue, as it makes accurately registering 
the EPI to the T1w image problematic.  Some folks have made use of an "average 
field map" to attempt to improve upon this situation, but I don't have this 
code or personal experience with this.

Lacking the T2w image need not necessarily prevent mapping fMRI data to CIFTI 
as one can take the non T2w parts of PreFreeSurfer (basically everything except 
the T2w to T1w registration and the bias correction), do things like specifying 
the T1w image as the T2w image (e.g. for the MNI registration), run FreeSurfer 
on its own, and then specify the T1w image as the T2w image for PostFreeSurfer. 
 A script that does all of this exists, but is not an "official pipeline."

Peace,

Matt.

From: Kelli Cannon >
Date: Monday, October 3, 2016 at 5:32 PM
To: "hcp-users@humanconnectome.org" 
>
Cc: Matt Glasser >
Subject: Converting legacy data to CIFTI format

Hello,

I would like to convert a legacy dataset into CIFTI format. The legacy dataset 
lacks T2-weighted images or field maps. How does the HCP advise that 
investigators go about converting legacy data into CIFTI format? I assume this 
must be possible, as we can use FreeSurfer to convert to flat maps with such 
data...

For the structural data, the PreFreeSurfer pipeline requires both a T1w and a 
T2w image, so it can not be used on the legacy dataset. One can run the T1w 
images through FreeSurfer's recon-all to approximate the HCP FreeSurfer 
pipeline for lower-resolution data. However, the PostFreeSurfer pipeline 
requires additional input files (e.g., T1w_acpc_dc_restore.nii.gz) that are not 
included in the FreeSurfer output.

Is there a reasonably straightforward way of converting legacy data without T2w 
images into CIFTI format? If not, does HCP plan to create a pipeline for 
preprocessing legacy data?


Best regards,

Kelli Cannon
Graduate Student
UAB Department of Vision Science
kecan...@uab.edu



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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